I think that you have a good idea, but keep in mind that you are really going to get what you pay for. If you do something like rattle-can it, for example, you won't have UV protection and the paint won't last very long, or protect well from rust, essentially wasting your money. Also, a decent basecoat/ clearcoat job wil cost more than you are wanting to spend, but it will offer the protection that you need. If I were you I would either bump up the budget a little, or maybe even consider a single stage paint job, which will be cheaper than BC/CC, but will give you pretty much all of the benefits. Just my 2 cents.
'94 YJ: 4.0L HO fi, 5-speed AX-15, Daystar 1.25" shackles, 17" JK wheels, lined tub, custom paint, Bestop Supertop, etc..
'88 YJ: 4.2L carb, 5-speed, stock everything. Banana-ish yellow. hard top. 26,XXX original miles.